I started over from the .dcm and I didn't encounter the error anymore. So
alls well.
-
Josh
On Sun, Aug 19, 2012 at 11:54 PM, Joshua Lee wrote:
> Hi All,
>
> I tried to convert a high res T2 image using mri_convert and got this
> error message:
>
> nifti1Read(): unsupported slice timing pattern
Thanks for your answers!
Following your comments, I have thought to select only first two sequences,
as they are the more frequent in our database and only differ on the TE
parameter. We will also create balanced groups.
cheers
Daniel
2012/8/18 Andre van der Kouwe
> Hi Daniel,
>
> I agree, t
Doug,
I edited the dura from the brain.finalsurfs.mgz file using the command tkmedit
(subject ID) brain.finalsurfs.mgz -aux T1.mgz -surfs and going through the
necessary slices that need fixing and erase the dura. I then ran this subject
with the command recon-all -subjid (subject ID) -autoreco
Thanks Bruce. I see that because these are not Siemens scans I need to use
the command dcmunpack instead of unpacksdcmdir, however, if the DICOM
files are already saved on our cluster do the files need to be unpacked or
simply converted to COR format using mri_convert? Thanks!
Best,
Alex
> Hi Al
what do you mean "compute a gaussian image"?
doug
On 08/18/2012 05:01 PM, John Papaioannou wrote:
> Hi Doug,
>
> Will the following compute a gaussian image?
>
> mri_fwhm --smooth-only --fwhm 2 --i brainmask.mgz --o
> brainmasksmoothed.mgz
>
> Thank you in advance,
> John
> ___
>
> JohnPapaioanno
By default, it uses nearest neighbor. There is an option to use trilinear.
doug
On 08/19/2012 04:23 AM, Xinian Zuo wrote:
> Dear Dr. Greve,
>
> Hope all is well. I am writing to ask if you can give me some
> references or details on the interpolation method used in FS (version
> 5.1) cmd mri_vol2s
dcmunpack will convert them to whatever file format you want (don't use
COR though).
doug
On 08/20/2012 09:51 AM, Alexandra Tanner wrote:
> Thanks Bruce. I see that because these are not Siemens scans I need to use
> the command dcmunpack instead of unpacksdcmdir, however, if the DICOM
> files ar
Hi Doug,
Thanks! Do you know what command line I should use with dcmunpack? I can't
specify the run number since I don't currently have that information for
my scan, only the DICOM files. Typically when we unpack our Siemens files
we use the following command line: "unpacksdcmdir -src -targ
-run
You can look at the help (dcmupack -help) for info, but basically you
run it twice. First
dcmunpack -src dicomdir
This will give you a list of runs,
then run it specifying the runs that you want to unpack. It takes the
same command line options as unpacksdcmdir
doug
On 08/20/2012 10:05 AM, Alexa
Fidel,
I don't know why those files are missing from the Tiger ppc distribution,
but i confirmed that indeed they are. Here is a tarball of the
distribution which contains everything:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/freesurfer-Darwin-tiger-ppc-stable-pub-v5.1.0.tar.gz
Hi Cyrus, my apologies, I told you to edit the wrong file. You should
edit brainmask.mgz, not brainmask.finalsurfs.mgz. Sorry about, I hope
you did not waste too much time.
doug
On 08/20/2012 09:31 AM, Sarosh, Cyrus wrote:
> Doug,
>
> I edited the dura from the brain.finalsurfs.mgz file using th
The problem with the ICV calc in v5.1 is explained in the v5.1 Known
Issues section of the ReleaseNotes page, which i've also just updated
with notes on a workaround:
https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes
the workaround is to type these commands:
cd subjid/mri
talairach_avi --i
Dear Doug,
As I mentioned in a previous email, I'm currently working with T1 DICOM
files from the Clinical PACS System that I'd like to pull into the
freesurfer stream to get cortical thickness. I've unpacked the data,
converting the DICOM files to mgz format, and successfully ran the first
recon-
Dear FreeSurfers,
I have been working on cross-sectional MRI's of healthy older adults
(55-88), and have been correcting the FreeSurfer 5.1 output using the
instructions given here (
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData) to
correct the FreeSurfer errors that we h
Hi,
I was wondering if there is a way to run statistical tests, such as a
2-way ANCOVA, on QDEC but without the interaction effect. I ran a 2-way
ANCOVA for thickness measures for a longitudinal study, and no interaction
effect was found. Therefore, I would like to run the same test but without
t
Hi Mark,
Try either one of these options for uploading data or snapshots for us to
look at.
FTP info:
https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
E-mail file drop:
https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
-Louis
On Mon, 20 Aug 2012, Mark Fletcher wrote:
De
Hi Mark,
Did you see my post from 1/10/2012 ("anterior temporal lobe problems")?
We had good success (albeit not perfect) in improving our anterior
temporal surfaces using the options mentioned there.
cheers,
-MH
On Mon, 2012-08-20 at 14:43 -0500, Mark Fletcher wrote:
> Dear FreeSurfers,
>
> I
And for fixing this in the longitudinal stream this should work:
1. you can fix the cross runs as described below (not really necessary,
as the longitudinal results do not depend on this)
2. fix the base:
cd /mri
talairach_avi --i nu.mgz --xfm transforms/talairach.xfm
recon-all -base -tp -tp .
Hi Doug and Freesurfer team,
I am trying to coregister some PET maps with their relative high resolution
MEMPRAGE files.
I was thinking that bbregister might be my best option but the results are
still not satisfactory, likely due to the intrinsic features of my radioligand
(the resulting maps
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